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Study units can occur either in parallel or sequentially. An example of the parallel occurrence of study units is when administrative data collection occurs at the same time as questionnaire data collection. These study unit paths might be split following an initial study unit and later joined before another study unit proceeds. During the join, an integration data processing pipeline might be inserted.

Study units are included in a protocol specification using the StudyUnitControl. A StudyUnitControl references a study unit. A StudyUnitControl takes inputs and outputs. Inputs to a study unit might come from the study's archive. Outputs from study units might be deposited in the archive.

Additionally, protocol specification includes the specification of the arrangement of instruments within a study unit. For example in a longitudinal study at a visit several instruments might be administered. They might administered in a sequence with conditions, in any order or in some combination of sequence and any order. The protocol specification orchestrates the order of instruments within a study unit.

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Instruments are included in a protocol specification using InstrumentControl. InstrumentControl references an instrument. An InstrumentControl takes inputs and outputs. Inputs to an instrument can include "preloads". Outputs from an instrument can include "critical data items" that figure into subsequent control constructs that play a role in the flow of instruments.